Ensure refs are updated from their origin

It can happen that a related ref is installed from a different remote
than the thing it's related to. We always want to update things from
their origin remote. However as of now FlatpakTransaction resolves the
commit of a related ref to the one available from the main ref origin,
and later sets the remote for the operation to the installed origin (see
commit 6793d90b). In case there is a newer commit in the main ref
origin than the installed origin, this leads to an update operation
being erroneously created, only to then error out with an HTTP 404
error, because the commit from the main ref origin is being pulled from
the installed ref origin. For specific steps to reproduce see
https://github.com/flatpak/flatpak/issues/3128#issuecomment-948948040

So, ensure that when a FLATPAK_TRANSACTION_OPERATION_INSTALL_OR_UPDATE
operation is created for something that's installed, whether it's a
related ref or something else, the remote used is always the origin. And
ensure that the remote is set correctly before the stage where the op is
resolved to a commit, to avoid the situation described above. This is
essentially a re-implementation of the fix in commit 6793d90b.

Also, add a unit test for this behavior.

This commit also makes a few changes to documentation to make it clear
that this related-ref-different-origin situation is possible.

Fixes #3128

(cherry picked from commit 49d9052d2248de8b5f3c4c1c6ca7dfceefcbcd2f)
(only merge conflicts in tests/testlibrary.c)